Monday, March 12, 2007

DNA databases and DNA profiling   posted by the @ 3/12/2007 07:25:00 PM

Everything I've read about DNA profiling and DNA databases suggests the following:
  1. A universal national DNA database should be constructed
  2. DNA profiling for this database should switch to SNP genotyping
DNA database - The U.S. national and state governments operate a number of DNA databases. Most law enforcement databases are integrated under the FBI's CODIS system, which now contains several million DNA profiles in its "offender" index. Privacy advocates raise a number of concerns about these databases, but most political action concerns the criteria for getting profiles into and out of these databases. As far as I can tell, all of the concerns about inclusion/exclusion criteria would be circumvented by the existence of a universal database. For example, issues of contention include:
  • What crimes warrant the collection of DNA?
  • Should DNA be automatically collected at arrest or not until conviction?
  • If DNA is collected at arrest, should DNA profiles be expunged if no conviction is made?
  • Does the mass collection of DNA raise the risk of false positives and subsequent false convictions? [Note, ostensibly it does - especially when imperfect forensic profiles are used to search for a match.]
The retention of DNA samples is a second concern for privacy advocates. This is a real issue which should be addressed by maximizing protections of stored samples or by choosing to discard samples. Other concerns are aimed at the application of DNA databases in criminal prosecution. These criticisms exist regardless of the databases' size/scope, but there is reason to believe that the increased attention to the caveats of DNA evidence that a universal database provides would improve these conditions. Along those lines, there are a number of benefits which come from universal coverage:
  • Universal coverage is perhaps the best way to ensure proper privacy protection and oversight of the database.
  • False positives would be more easily detected and corrected.
  • The advantages to law enforcement would be obvious.
  • Paternity would be known for all children.
  • It would have beneficial uses for identification outside of law-enforcement.
DNA profiling - The most common form of DNA profiling used for DNA databases (and other DNA-identification applications) is STR genotyping. Even with the best foreseeable technological advancements, STR genotyping has many disadvantages to SNP genotyping. If we were to implement a universal DNA database, it would be prudent to make the switch to SNP genotyping.
  • While STR genotyping is currently performed on ~13-16 highly polymorphic loci, it would be technically trivial to genotype hundreds (or thousands or more!) of biallelic SNPs.
  • High-throughput SNP genotyping platforms are advanced, and the pace of development (i.e. reduction in costs) is enormous.
  • SNP genotyping is technically simpler than STR genotyping, and it would be easier to miniaturize.
  • Huge databases of SNPs are already known, making it possible to select a panel of SNPs to meet almost any reasonable requirements. For example, SNPs could be chosen to minimize the chance that they are actually markers for socially-important phenotypic differences between individuals or groups.
  • Multiple correlated SNPs can be chosen for redundancy against genotyping error.
  • Poor quality forensic samples can be more accurately assigned to database profiles when there are hundreds (or thousands) or points of comparison, in contrast to the 13 STRs used in CODIS.
  • You can imagine the on-demand genotyping of a select subset of SNPs as an identity-verification scheme.
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